When a person dies, that person move to towards a situation he believed in just before death.
For example, just after death, a good Christian may see Jesus, a Muslim who feels he has done good will see Mohammed. A Hindu may see Lord Krishna or any of their deities.
There are those who believe there are going to Hell and they will see themselves in Hell in the beginning.
However, this is the initial reality and it will change as soon as one slowly realizes who God is. This reality will evolve until one comes to be with God as who God really is in Heaven. This is what will happen to Muslims, Christian, Hindus, Buddhists, atheists, and other persons from every belief system. In the end we will all end up in heaven with God. This includes atheists, and even those who thought they are bound to go the Hell.
Therefore, yes, atheist will eventually go to heaven like all the others. It is a matter of realizing the ultimate truth. All paths lead towards God. Do not be concerned over atheists, God's plan is so grand that no one will be lost. However, there are those who believe that God cannot be good as this.